MultiDataSet 1.11.0
Carlos Ruiz-Arenas
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MultiDataSet |
| Branch: master |
| Last Commit: bafaaa3 |
| Last Changed Date: 2018-10-30 11:54:36 -0400 (Tue, 30 Oct 2018) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | [ ERROR ] | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r MultiDataSet -R && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data MultiDataSet
###
##############################################################################
##############################################################################
* checking for file 'MultiDataSet/DESCRIPTION' ... OK
* preparing 'MultiDataSet':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'MultiDataSet.Rmd' using rmarkdown
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
rowSums, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
--- finished re-building 'MultiDataSet.Rmd'
--- re-building 'MultiDataSet_3party_Integration.Rmd' using rmarkdown
Warning in add_eset(object, gexpSet, dataset.type = "expression", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
Warning in add_eset(object, gexpSet, dataset.type = "expression", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
Warning in add_eset(object, gexpSet, dataset.type = "expression", GRanges = range, :
No id column found in pData. The id will be equal to the sampleNames
Warning in add_rse(object, methySet, dataset.type = "methylation") :
No id column found in colData. The id will be equal to the sampleNames
Loading required package: ade4
Attaching package: 'ade4'
The following object is masked from 'package:Biostrings':
score
The following object is masked from 'package:GenomicRanges':
score
The following object is masked from 'package:IRanges':
score
The following object is masked from 'package:BiocGenerics':
score
Quitting from lines 241-242 (MultiDataSet_3party_Integration.Rmd)
Error: processing vignette 'MultiDataSet_3party_Integration.Rmd' failed with diagnostics:
there is no package called 'iClusterPlus'
--- failed re-building 'MultiDataSet_3party_Integration.Rmd'
--- re-building 'MultiDataSet_Extending_Proteome.Rmd' using rmarkdown
Warning in MultiDataSet::add_eset(object, protSet, dataset.type = "proteome", :
No id column found in pData. The id will be equal to the sampleNames
--- finished re-building 'MultiDataSet_Extending_Proteome.Rmd'
SUMMARY: processing the following file failed:
'MultiDataSet_3party_Integration.Rmd'
Error: Vignette re-building failed.
Execution halted